There have been interviews where Whedon has mentioned writing a script for a fifth film. Not sure it would necessarily be good, though.
It would've probably been around the time of the first 'Buffy The Vampire Slayer' series. As someone who became a fan of that show, I'd say the first had a few glimmers of intrigue, but that the writing, itself, didn't get truly amazing until the second and third (after which, sadly, it never quite recaptured those heights; possibly because that was around the time he split his focus between that and the 'Angel' spin-off show, then 'Firefly'). The second, especially. It's easy to dismiss the guy as not having much talent when you only go by stuff like 'Alien Resurrection', but there were some moments of genuine brilliance in the second and third series of BTVS, where the balance between emotional drama, action and moral consequences was just perfect.
I've still yet to see most episodes of 'Firefly', but the film, 'Serenity', was paced and written well for a science-fiction film.
So, in reflection of all that, I'd suspect his fifth film's script would've still probably felt a lot like AR. Would still have had that unfortunately superficial comic book feel. It just strikes me as that being his period for that sort of style. If he'd done it around 1998/1999, there is a chance it would've been better. He was writing in a much more realistic tone around then, even when dealing with extraordinary subjects.
Sadly, he's never been able to write for the military without portraying it as ridiculous (this extends to even the canon 'Buffy The Vampire Slayer' comics he wrote). If he included any such aspect to the fifth film's script, I don't think it would've gone over well. He deals a lot better when the military is left in the background.
Strangely, he said in an interview that, a little while back, a fan pointed out to him how the Betty crew and the one represented in 'Firefly' were so alike and that he never realised until then. I always thought it was obvious, but just goes to show that he can sometimes let his old work bleed into new and not realise it.